I could be wrong, but I genuinely believe the problem with your line of reasoning is you're rationalizing for a system that benefits you. Your ideology benefits from how things are, and so you find reasons to justify why the way things are is good, actually.
If say states had been divided up differently, would your entire belief system crumble? Assume city-states were the norm and the Senate was overwhelmingly controlled by whichever party controlled urban populations. Like say North Carolina got divided into Raleigh-Durham, Charlotte, the Triangle, Wilmington, and the rest of the state as just one big territory. And every state was like this.
Would you suddenly say hey this is a bad system, not because it benefits people I don't agree with, but because of some other silly reason?
What is so magical about lines put on maps by our great-great-great grandfathers?
If there was a magical US with three states, two with only 1 citizen and one with 1,000,000, would you still hold by your principle that they have their own governments that federate with those of states so this is good?
Where in your system do you draw the line and make a distinction between fair and unfair? How do you determine if one arrangement is more fair than another? Why would you not push for the most fair arrangement?
My principle is embarrassingly simple. Political power should be equal to the number of people represented. That's it. Easy to explain, easy to grasp, easy to measure whether something is fair or unfair. It's imperfect--Lord knows population majorities can still be bastards--but it's the best, most egalitarian system created. And, importantly, it's a principle that doesn't change just because it doesn't benefit me. You're right, it's not very nuanced. Simple often works best.